1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
|
#include <BALL/KERNEL/molecularInteractions.h>
using namespace BALL;
using std::map;
using std::make_pair;
bool MolecularInteractions::SAVE_ONLY_SUMS = 0;
MolecularInteractions::MolecularInteractions()
{
total_energy_ = 0;
threshold_ = 0.01; // by default save only interaction with strength >= 10 J/mol
}
void MolecularInteractions::clear()
{
interactions_map_.clear();
interaction_energies_.clear();
total_energy_ = 0;
}
void MolecularInteractions::setThreshold(double threshold)
{
threshold_ = fabs(threshold);
}
void MolecularInteractions::addInteraction(const Atom* atom, String interaction_type, double energy)
{
total_energy_+=energy;
map<String,double>::iterator s1 = interaction_energies_.find(interaction_type);
if(s1==interaction_energies_.end())
{
interaction_energies_.insert(make_pair(interaction_type,energy));
}
else
{
s1->second+=energy;
}
if(SAVE_ONLY_SUMS) return;
if(fabs(energy)>=threshold_)
{
map<String, map<const Atom*,double> >::iterator search_it = interactions_map_.find(interaction_type);
if(search_it==interactions_map_.end())
{
map<const Atom*,double> new_map;
interactions_map_.insert(make_pair(interaction_type,new_map));
search_it = interactions_map_.find(interaction_type);
}
search_it->second.insert(make_pair(atom,energy));
}
}
void MolecularInteractions::addInteraction(String interaction_type, double energy)
{
total_energy_+=energy;
map<String,double>::iterator s1 = interaction_energies_.find(interaction_type);
if(s1==interaction_energies_.end())
{
interaction_energies_.insert(make_pair(interaction_type,energy));
}
else
{
s1->second+=energy;
}
}
bool MolecularInteractions::hasInteraction(const Atom* atom, String interaction_type) const
{
map<String, map<const Atom*,double> >::const_iterator search_it = interactions_map_.find(interaction_type);
if(search_it==interactions_map_.end()) return false;
return search_it->second.find(atom)!=search_it->second.end();
}
double MolecularInteractions::getInteractionEnergy(const Atom* atom, String interaction_type) const
{
map<String, map<const Atom*,double> >::const_iterator search_it = interactions_map_.find(interaction_type);
if(search_it==interactions_map_.end()) return 0;
map<const Atom*,double>::const_iterator s2 = search_it->second.find(atom);
if(s2==search_it->second.end()) return 0;
else return s2->second;
}
double MolecularInteractions::getInteractionEnergy(const Atom* atom, const list<String>& interaction_types) const
{
double energy = 0;
for(list<String>::const_iterator it=interaction_types.begin(); it!=interaction_types.end(); it++)
{
energy+=getInteractionEnergy(atom,*it);
}
return energy;
}
const map<const Atom*,double>* MolecularInteractions::getInteractions(String interaction_type) const
{
map<String, map<const Atom*,double> >::const_iterator search_it = interactions_map_.find(interaction_type);
if(search_it!=interactions_map_.end()) return &search_it->second;
else return NULL;
}
void MolecularInteractions::getInteractions(const list<String>& interaction_types, map<const Atom*,double>& interactions) const
{
for(list<String>::const_iterator s_it=interaction_types.begin(); s_it!=interaction_types.end(); s_it++)
{
const map<const Atom*,double>* map_s = getInteractions(*s_it);
if(!map_s) continue;
if(s_it==interaction_types.begin())
{
interactions = *map_s;
continue;
}
for(map<const Atom*,double>::const_iterator it=map_s->begin(); it!=map_s->end(); it++)
{
map<const Atom*,double>::iterator search_it=interactions.find(it->first);
if(search_it==interactions.end())
{
interactions.insert(make_pair(it->first,it->second));
}
else
{
search_it->second+=it->second;
}
}
}
}
double MolecularInteractions::getInteractionEnergy(String interaction_type) const
{
map<String,double>::const_iterator s1 = interaction_energies_.find(interaction_type);
if(s1!=interaction_energies_.end())
{
return s1->second;
}
else return 0;
}
double MolecularInteractions::getInteractionEnergy(const list<String>& interaction_types) const
{
double energy=0;
for(list<String>::const_iterator it=interaction_types.begin(); it!=interaction_types.end(); it++)
{
energy += getInteractionEnergy(*it);
}
return energy;
}
double MolecularInteractions::getInteractionEnergy() const
{
return total_energy_;
}
|
